About GenomeForge-Pro

GenomeForge-Pro is a public web platform for the assembly of genomes from sequence reads for prokaryotes or bacteria.

Currently, we only support Illumina short reads. We implement several well-known methods and tools such as Shovill and Unicyler.

Here's an example job output here.

Submit your job

STEP 1: Provide an input

GenomeForge-Pro takes forward and reverse reads in FASTQ format. You can either provide run accessions or upload your own reads via the drag and drop or upload buttons.

OPTION A: Provide a list of run accessions [SRR#, ERR#, DRR#]

OPTION B: Upload a text file with a list of run accessions

OPTION C: Upload paired-end reads [#1.fastq(.gz) and #2.fastq(.gz)]

Drag and drop files here or click to select

STEP 2: Select an assembly method

Once an accession is provided or read files are selected, you can select the assembler of your choice.

Shovill (SPAdes)
Default choice for most bacterial isolate Illumina read sets. Shovill uses SPAdes with read cleaning, depth normalisation, stitching, and post-assembly correction.

Shovill (Megahit)
Usually faster than SPAdes and useful for quick draft assemblies, but Shovill notes that faster alternatives can produce less complete assemblies.

Shovill (Velvet)
A legacy de Bruijn graph assembler. Use when you need comparison with older workflows rather than as the first-choice modern assembly.

Shovill (SKESA)
Fast and conservative. Good when avoiding risky joins matters; some Shovill correction stages may be less necessary because SKESA is already conservative.

Unicycler (SPAdes)
For Illumina-only jobs, Unicycler optimises SPAdes assembly graphs, filters low-depth graph parts, and rejects lower-confidence repeat resolutions.

STEP 3: Clear or hit Submit

About GenomeForge-Pro

Submit your job

Contact us